# Text file created by Jesse Bloom, 2007.
#
# This file contains data on temperature-sensitive (ts) mutations to the hemagglutinin 
# molecule of the A/WSN/33 (H1N1) influenza virus, as well as mutations that suppress
# the ts phenotype.  The relevant references are:
#   [1] N Tong, K Nakajima, and S Nakajima, "Identification of the sites for 
#       suppressor mutations on the hemagglutinin molecules to temperature-
#       sensitive phenotype of the influenza virus," Microbiol Immunol, 39:687-692 
#       (1995)
#   [2] AL Hiti, AR Davis, and DP Nayak, "Complete sequence analysis shows that the
#       hemagglutinins of the H0 and H2 subtypes of human influenza virus are closely
#       related," Virology, 111:113-124 (1981)
#   [3] S Nakajima, DJ Brown, M Ueda, K Nakajima, A Suigiura, AK Pattnaik, and DP
#       Nayak. "Identification of the defects in the hemagglutinin gene of two
#       temperature-sensitive mutants of A/WSN/33 influenza virus." Virology,
#       154:279-285 (1986)
#   [4] M Ueda and A Sugiura. "Physiological characterization of influenza virus
#       temperature-sensitive mutants defective in the haemagglutinin gene."
#       J Gen Virol, 65:1889-1897 (1984)
#   [5] DA Simpson and RA Lamb. "Influenza virus ts61S is significantly defective
#       in polypeptide folding and intracellular transport at the permissive
#       temperature." Virology, 185:477-483 (1991).
#
# Here is a brief summary of what these references say.  Reference [4] characterizes two
# ts mutants of HA (which from here on is taken to refer to the hemagglutinin
# of the A/WSN/33 influenza strain) that appear to be defective in transport
# beyond the Golgi apparatus, and which also are heat sensitive.  These two
# mutants (ts-61S and ts-134) do not possess HA activity at 39.5 degrees, but
# do at 34 degrees.  The two ts mutants are also rapidly inactivated at 51 degrees.
# According to reference [5], ts-61S is actually also partially impaired in transport
# even at the permissive temperature.  In any case, references [1] and [3] actually
# identify the exact mutations responsible for the ts phenotypes.  In [1] and [3],
# the amino acids are numbered according to the numbering scheme defined in [2],
# in which the first residue (Met) is numbered as -17, and the numbers progress up
# to -1, and then to 1.  In this numbering scheme, the ts-61S mutation is due to
# S110P, and the ts-134 mutation is due to Y157H (actually, [3] reports this mutation
# as Y159H, but after comparing to the sequence and [1] I am almost certain that this
# is an error, and that it is actually Y157H as reported in [1]).  Reference [3]
# also identifies a single mutation that reverts ts-61S; this is a mutation to the 
# same amino acid (S110L).  Reference [3] also identifies a few mutations that revert
# ts-134.  These revertants to ts-134 from [3], as well as a much more extensive
# listing of revertants, are given in [1].  Both [1] and [3] also characterize
# whether the mutations restore the HA thermostability as well as revert the ts
# phenotype.
#
# Below, I have listed all of these mutations and described their phenotypes.  For
# each mutation, the following information is given:
#   TS_REVERTANT - in this category, each mutation is classified as either "TS"
#      if it causes a temperature-sensitive phenotype, or "REVERTANT" if it
#      reverts a temperature-sensitive phenotype caused by another mutation.
#   STABILITY - the stability change caused by the mutation.  References [1] and [3]
#      categorically classify mutations as causing a large drop in stability (these
#      are the ts mutants), restoring a large drop in stability (these mutations
#      are labeled as "Stable" in Table 1 of [1], partially restoring a large drop
#      in stability (these are labeled as "Intermediate" in Table 1 of [1]), or
#      causing no apparent change in stability (these are labeled as "Unstable" in
#      Table 1 of [1]).  I have converted these categories to numerical values:
#          -2 = Stable
#          -1 = Intermediate
#          0 = Unstable
#          2 = temperature sensitive mutation
#   ORIGINAL_MUTATION - the mutation as labeled in the original reference, using
#      the numbering scheme of [2].
#   RENUMBERED_MUTATION - the mutation labeled in a renumbered sequential scheme in which
#      the first residue (Met) is numbered 0, the second residue is 1, and so on up to
#      the final Ile being numbered 364.
#   COMMENTS - any comments about the mutation, preceded by a "#" character.
#   1RVZ_NUMBER - residue number of aligned residue in PDB structure 1RVZ;
#       the wildtype identities have been changed to match those in the PDB structure.
#   1RVZ_CHAIN - the chain (HA1 or HA2) to which the residue belongs in PDB structure 1RVZ.
#       Chain HA1 is PDB chains A, C, E; HA2 is PDB chains B, D, F.
#
#TS_REVERTANT   STABILITY  ORIGINAL_MUTATION    RENUMBERED_MUTATION 1RVZ_NUMBER 1RVZ_CHAIN  COMMENTS
TS  2   S110P   S126P   S114P   HA1 # mutation responsible for the temperature sensitivity of ts-61S, reported in [3]
TS  2   Y157H   Y173H   Y161H   HA1 # mutation responsible for the temperature sensitivity of ts-134, reported in [1]
REVERTANT   -1      I3L     I19L    I7L HA1 # ts-134 revertant Rts133 from Table 1 of [1]
REVERTANT   -2      F20S    F36S    L24S    HA1 # ts-134 revertants Rts103, Rts110, Rts122 from Table 1 of [1]    
REVERTANT   -2      E21G    E37G    D25G    HA1 # ts-134 revertant Rts135 from Table 1 of [1]
REVERTANT   -2      A25T    A41T    A29T    HA1 # ts-134 revertants Rts107, Rts121, Rts125, Rts131 from Table 1 of [1], already mutated to T in 1RVZ
REVERTANT   -1      Q51H    Q67H    Q55H    HA1 # ts-134 revertants Rts113, Rts146, Rts151 from Table 1 of [1]
REVERTANT   -2      T58A    T74A    T62A    HA1 # ts-134 revertant Rts106 from Table 1 of [1], already mutated to A in 1RVZ
REVERTANT   -2      T58I    T74I    T62I    HA1 # ts-134 revertant Rts134-3 from Table 1 of [1], already mutated in to A in 1RVZ
REVERTANT   0       P72S    P88S    P76S    HA1 # ts-134 revertants Rts128, Rts130 from Table 1 of [1]
REVERTANT   0       P72T    P88T    P76T    HA1 # ts-134 revertant Rts134-7 from Table 1 of [1]
REVERTANT   0       S192G   S208T   Q196T   HA1 # ts-134 revertants Rts105, Rts119, Rts123, and Rts155 from Table 1 of [1]
REVERTANT   -1      D221G   D237G   D225G   HA1 # ts-134 revertants Rts144, Rts153, Rts 134-2 from Table 1 of [1]
REVERTANT   0       F260L   F276L   F264L   HA1 # ts-134 revertant Rts148 from Table 1 of [1]
REVERTANT   -1      M343L   M359L   M517L   HA2 # ts-134 revertants Rts114, Rts149, and Rts 134-1 from Table 1 of [1]
REVERTANT   -1      I344V   I360V   I518V   HA2 # ts-134 revertant Rts124 from Table 1 of [1]
REVERTANT   -2      G373R   G389R   G547R   HA2 # ts-134 revertants Rts112, Rts118, Rts129, Rts140, Rts141, Rts145, Rts147, Rts152, Rts154, Rts156 from Table 1 of [1]
REVERTANT   -2      M385I   M401I   M559I   HA2 # ts-134 revertants Rts127 from Table 1 of [1]
